[Biopython-dev] BWA Wrapper

[Saket Choudhary]

In short , am I allowed to play with this extra parameter thing as per
the code standards of biopython ?

On 14 February 2013 22:34, Saket Choudhary <saketkc at gmail.com> wrote:
> I was thinking of adding one more parameter to the _call function, lets say
> 'stdout_to_filepath'.
> If this is set then I add one more if condition here  to set the stdout as
>
>
> stdout_arg = open(stdout_to_filepath, "w")
>
> I tried it and it did work, but I am not sure if it  this standard can be
> incorporated in the biopython codebase ?
>
> Thanks
>
> Saket
>
>
> On 14 February 2013 21:49, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>
>> On Thu, Feb 14, 2013 at 4:02 PM, Saket Choudhary <saketkc at gmail.com>
>> wrote:
>> > Theres one more issue that I have run into . Consider the following
>> > command
>> > , the outout generated is written by piping it to a file called
>> > aln_sa.sai,
>> >
>> > bwa aln database.fasta short_read.fastq > aln_sa.sai
>> >
>> > Now if we look into the _call method here , it takes as its inout a
>> > boolean
>> > for stdout. So should I modify this so that it can take 'stdout' as on
>> > opened file  instance which I can invoke while unvoking my
>> > BwaAlnCommandLine
>> > functions as follwos:
>> >
>> > a=BwaAlnCommandLine()
>> > b=a(stdout=open("aln_sa.sai","wb"))
>>
>> Is that possible?
>>
>> For complex use of subprocess and pipes, we've previously recommend
>> the user handle this explicitly themselves, just use str() on the command
>> line wrapper object to get 'bwa aln database.fasta short_read.fastq' in
>> this
>> case. There are some examples in the Tutorial with (multiple sequence)
>> alignment tools.
>>
>> Peter
>
>